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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
HiC-Pro Resource Report Resource Website 100+ mentions |
HiC-Pro (RRID:SCR_017643) | software application, data processing software, software resource, workflow software | Software tool as optimized and flexible pipeline for Hi-C data processing. Used to process Hi-C data, from raw fastq files, paired end Illumina data, to normalized contact maps. | Hi-C, data, raw, fastq, file, paired, Illumina, normalized, contact, map, bio.tools |
is listed by: Debian is listed by: bio.tools |
France Genomique National infrastructure ; Labex Deep ; European Research Coucil ; ERC Advanced Investigator award ; European Commission ; ABS4NGS project ; National Human Genome Research Institute ; Paris Alliance of Cancer Research Institutes ; Howard Hughes Medical Institute |
PMID:26619908 | Free, Available for download, Freely available | biotools:hic-pro | https://bio.tools/hic-pro | SCR_017643 | 2026-02-17 10:03:16 | 206 | ||||||
|
OrthoFinder Resource Report Resource Website 1000+ mentions |
OrthoFinder (RRID:SCR_017118) | data analysis software, software application, data processing software, software resource | Software Python application for comparative genomics analysis. Finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of gene duplcation events in those gene trees, infers rooted species tree for species being analysed and maps gene duplication events from gene trees to branches in species tree, improves orthogroup inference accuracy. Runs set of protein sequence files, one per species, in FASTA format. | comparative, genomic, analysis, find, orthogroup, ortholog, infer, gene, tree, duplicate, accuracy, protein, sequence, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Bill and Melinda Gates Foundation ; UKAID |
PMID:26243257 DOI:10.1101/466201 |
Free, Available for download, Freely available | biotools:OrthoFinder, OMICS_09733, BioTools:OrthoFinder | https://bio.tools/OrthoFinder https://bio.tools/OrthoFinder https://bio.tools/OrthoFinder |
SCR_017118 | OrthoFinder2, OrthoFinder | 2026-02-17 10:03:32 | 2899 | |||||
|
tximport Resource Report Resource Website 50+ mentions |
tximport (RRID:SCR_016752) | data analysis software, software application, data processing software, software resource | Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis. | pseudoaligned, reads, R, differential, expression, analysis, gene, transcript, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools works with: edgeR works with: DESeq2 |
SNSF 143883; European Commission ; NCI T32 CA009337 |
DOI:10.12688/f1000research.7563.1 | Free, Available for download, Freely available | biotools:tximport | https://bioconductor.org/packages/tximport/ https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html https://github.com/F1000Research/tximport https://bio.tools/tximport |
https://zenodo.org/record/35123#.W_w3behKiM8 | SCR_016752 | tximport v1.4.0 | 2026-02-17 10:02:45 | 91 | ||||
|
Nephele Resource Report Resource Website 10+ mentions |
Nephele (RRID:SCR_016595) | web application, production service resource, analysis service resource, service resource, software resource, data analysis service | Cloud based platform for simplified, standardized and reproducible microbiome data analysis. Allows users to process microbiome datasets through pipelines of existing software tools. | microbiome, datasets, process, analyze, metagenome, sequencing, data, bio.tools |
uses: mothur uses: QIIME uses: biobakery uses: A5-miseq is listed by: NIAID is listed by: bio.tools is listed by: Debian has parent organization: OCICB |
NIH Department of Health and Human Services GS35F0373X | PMID:29028892 | Free, Available for download, Freely available | biotools:nephele | https://github.com/niaid/Nephele https://bio.tools/nephele |
SCR_016595 | 2026-02-17 10:03:28 | 27 | ||||||
|
scanpy Resource Report Resource Website 100+ mentions |
scanpy (RRID:SCR_018139) | data analysis software, software application, data processing software, software resource | Software Python tool for large scale single cell gene expression data analysis. Integrates analysis possibilities of established R-based frameworks, provides pre processing, visualization, graph-drawing and diffusion maps, clustering, identification of marker genes for clusters via differential expression tests and pseudo temporal ordering via diffusion pseudo time. | Large scale, single cell, gene expression, data analysis, R, pre processing, visualization, graph drawing, diffusion map, clustering, marker gene, differential expression test, bio.tools |
uses: BBKNN is used by: triku is used by: MUON is listed by: Debian is listed by: bio.tools is related to: Anndata has plug in: infercnvpy |
Helmholtz Postdoc Programme ; German Research Foundation |
PMID:29409532 | Free, Available for download, Freely available | biotools:scanpy, BioTools:scanpy | https://icb-scanpy.readthedocs-hosted.com/en/stable/ https://bio.tools/scanpy https://bio.tools/scanpy https://bio.tools/scanpy |
SCR_018139 | Single Cell Analysis in Python | 2026-02-17 10:03:24 | 221 | |||||
|
DrivAER Resource Report Resource Website 1+ mentions |
DrivAER (RRID:SCR_019076) | data analysis software, software application, data processing software, software resource | Software tool as method for identification of driving transcriptional programs based on AutoEncoder derived Relevance scores. Infers relevance scores for transcriptional programs with respect to specified outcomes of interest in single-cell RNA sequencing data, such as psuedotemporal ordering or disease status.Used for manifold interpretation in scRNA-seq data. | Manifold interpretation, scRNAseq data, relevance scores infering, transcriptional program, psuedotemporal ordering, disease status, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:drivaer | https://bio.tools/drivaer | SCR_019076 | Driving transcriptional programs using AutoEncoder based Relevance scores | 2026-02-17 10:03:51 | 1 | |||||||
|
Epigenomics Workflow on Galaxy and Jupyter Resource Report Resource Website 1+ mentions |
Epigenomics Workflow on Galaxy and Jupyter (RRID:SCR_017544) | narrative resource, workflow, software application, data or information resource, data processing software, training material, data analysis software, software resource | Software tool as epigenomics analysis pipeline for analysis of ChIP-Seq and RNA-Seq data using Docker images containing Galaxy and Jupyter. | Epigenomic, analysis, pipeline, ChIP-Seq, RNA-Seq, data, Galaxy, Jupyter, bio.tools |
is listed by: bio.tools is listed by: Debian |
Agencia Estatal de Investigación of Spain SEV-2016-0672 (2017-2021) | Free, Available for download, Freely available | biotools:Epigenomics_Workflow_on_Galaxy_and_Jupyter | https://zenodo.org/record/3298029 https://bio.tools/Epigenomics_Workflow_on_Galaxy_and_Jupyter |
SCR_017544 | REA pipeline | 2026-02-17 10:03:15 | 2 | ||||||
|
IMGT HighV-QUEST Resource Report Resource Website 10+ mentions |
IMGT HighV-QUEST (RRID:SCR_018196) | alignment software, software application, data or information resource, production service resource, data processing software, analysis service resource, service resource, software resource, portal, image analysis software | Next generation B and T cell sequence alignment and characterization online surface by IMGT. Web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing. | Next generation sequencing, B cell, T cell, sequence alignment, immunoglobulin, antibody, T cell receptor, analysis, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian |
NHMRC ; MESR ; CNRS ; Université Montpellier 2 ; France ; GENCI |
PMID:22647994 PMID:23995877 PMID:22665256 |
Restricted | biotools:IMGt_HighV-QUESt | https://bio.tools/IMGT_HighV-QUEST | SCR_018196 | IMGT/HighV QUEST, IMGT/HighV-QUEST, IMGT web portal | 2026-02-17 10:03:43 | 11 | |||||
|
PM4NGS Resource Report Resource Website 1+ mentions |
PM4NGS (RRID:SCR_019164) | data management software, software application, workflow software, data processing software, data analysis software, software resource, software toolkit | Software tool to generate standard organizational structure for Next Generation Sequencing data analysis. Includes directory structure for project, several Jupyter notebooks for data management and CWL workflows for pipeline execution. | NGS workflow, standard organizational structure generation, Next Generation Sequencing data, NGS data analysis, NGS data analysis workflow, data integration, Jupyter notebook, CWL format, bio.tools |
is listed by: bio.tools is listed by: Debian |
Intramural Research Program of the National Library of Medicine NIH | DOI:10.7490/f1000research.1117155.1 | Free, Freely available | biotools:pm4ngs | https://bio.tools/pm4ngs | SCR_019164 | Project Manager for Next Generation Sequencing | 2026-02-17 10:03:37 | 1 | |||||
|
ngsRelate Resource Report Resource Website 1+ mentions |
ngsRelate (RRID:SCR_016588) | data analysis software, software application, data processing software, software resource | Software tool for estimating pairwise relatedness from next-generation sequencing data. | estimating, pairwise, relatedness, next, generation, sequencing, data, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools |
Danish National Research Foundation ; Danish Council for Independent Research |
PMID:26323718 | Free, Available for download, Freely available | biotools:ngsRelateV2, biotools:ngsrelate | https://bio.tools/ngsRelateV2 https://bio.tools/ngsrelate |
http://www.popgen.dk/software/index.php?title=NgsRelate&oldid=694 | SCR_016588 | ngsRelateV2 | 2026-02-17 10:03:26 | 6 | ||||
|
ComplexHeatmap Resource Report Resource Website 1000+ mentions |
ComplexHeatmap (RRID:SCR_017270) | software application, data processing software, data analysis software, software resource, data visualization software | Software package to arrange multiple heatmaps and support various annotation graphics. Used to visualize associations between different sources of data sets and to reveal potential patterns. | arrange, multiple, heatmap, visualize, data, pattern, genomic, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools |
German Cancer Research Center-Heidelberg Center for Personalized Oncology ; BMBF |
PMID:27207943 | Free, Available for download, Freely available | biotools:complexheatmap | https://github.com/jokergoo/ComplexHeatmap https://bio.tools/complexheatmap |
SCR_017270 | 2026-02-17 10:03:33 | 3266 | ||||||
|
SWISS-MODEL Resource Report Resource Website 1000+ mentions |
SWISS-MODEL (RRID:SCR_018123) | data access protocol, data or information resource, service resource, software resource, web service | Software tool as fully automated protein structure homology modeling server, accessible via ExPASy web server, or from program DeepView Swiss Pdb-Viewer. Structural bioinformatics web-server dedicated to homology modeling of 3D protein structures. Used to make protein modelling accessible to all biochemists and molecular biologists. | 3D protein structure, homology modeling server, protein modeling, structural bioinformatics, automated comparative modeling, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: ExPASy Bioinformatics Resource Portal is related to: Swiss-PdbViewerDeepViewv4.0 has parent organization: University of Basel; Basel; Switzerland provides: SWISS-MODEL Repository |
PMID:12824332 | Free, Freely available | biotools:swiss-model_workspace, biotools:swiss_model | https://bio.tools/swiss_model https://bio.tools/swiss-model_workspace |
SCR_018123 | 2026-02-17 10:03:44 | 2796 | |||||||
|
SIGNOR Resource Report Resource Website 10+ mentions |
SIGNOR (RRID:SCR_018485) | storage service resource, data or information resource, database, service resource, data repository | Software application to organize and store in structured format signaling information published in scientific literature. Information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. Each relationship is linked to literature reporting experimental evidence. Each node is annotated with chemical inhibitors that modulate its activity. Signaling information is mapped to human proteome. SIGNOR 2.0 stores manually annotated causal relationships between proteins and other biologically relevant entities including chemicals, phenotypes, complexes, etc with compliance to FAIR data principles. | Signal transduction data, signaling information, published data collection, activity flow, chemical inhibitor, human proteome, manually annotated data, protein, protein relationship, FAIR data, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: REDIportal |
Italian Association for Cancer Research ; ELIXIR-IIB ; Italian Node of the European ELIXIR infrastructure ; EMBL-EBI |
PMID:31665520 | Free, Available for download, Freely available | biotools:signor | https://bio.tools/signor | SCR_018485 | SIGnaling Network Open Resource, SIGNOR 2.0 | 2026-02-17 10:03:05 | 40 | |||||
|
SeqBuster Resource Report Resource Website 10+ mentions |
SeqBuster (RRID:SCR_009616) | data analysis software, software application, data processing software, software resource | Software tool for processing and analysis of small RNAs datasets.Reveals ubiquitous miRNA modifications in human embryonic cells. | small RNAs datasets, ubiquitous miRNA modifications, human embryonic cells, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Spanish Ministry of Health ; CIBERESP ; Sixth Framework Programme of the European Commission ; Spanish Ministry of Science and Innovation |
PMID:20008100 | Free, Available for download, Freely available | OMICS_00367, biotools:seqbuster | https://bio.tools/seqbuster | SCR_009616 | 2026-02-17 10:01:25 | 30 | ||||||
|
MACH Resource Report Resource Website 500+ mentions |
MACH (RRID:SCR_009621) | data analysis software, software application, data processing software, software resource | QTL analysis based on imputed dosages/posterior_probabilities. | genetic association, genomic analysis, imaging genomics, snp, gene, quantitative trait analysis, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Michigan; Ann Arbor; USA |
PMID:21058334 PMID:19715440 DOI:10.1002/gepi.20533 |
Free, Non-commercial, Acknowledgement requested | nlx_155856, biotools:mach | http://www.nitrc.org/projects/mach https://bio.tools/mach |
https://sources.debian.org/src/mach-haplotyper/ | SCR_009621 | mach2qtl, MaCH | 2026-02-17 10:01:30 | 925 | |||||
|
BEAST Resource Report Resource Website 5000+ mentions |
BEAST (RRID:SCR_010228) | software application, data processing software, data analysis software, sequence analysis software, software resource, software repository | A cross-platform software program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results. | bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is listed by: OMICtools is related to: TempEst is related to: BEAST2 is related to: PhyDyn has parent organization: University of Edinburgh; Scotland; United Kingdom |
DOI:10.1186/1471-2148-7-214 | nlx_156859, OMICS_04233, biotools:beast, SCR_015988 | http://www.nitrc.org/projects/beast-library https://bio.tools/beast https://sources.debian.org/src/beast-mcmc/ |
http://beast.bio.ed.ac.uk/Main_Page | SCR_010228 | BEaST Segmentation Library, Beast Software | 2026-02-17 10:01:47 | 6460 | ||||||
|
WEBLOGO Resource Report Resource Website 1000+ mentions |
WEBLOGO (RRID:SCR_010236) | data access protocol, service resource, web service, software resource | Web application to generate sequence logos, graphical representations of patterns within multiple sequence alignment. Designed to make generation of sequence logos easy. Sequence logo generator. | Generate sequence logo, pattern graphical representation, multiple sequence alignment, sequence logo generator, amino acid sequence alignment, nucleic acid sequence alignment, sequence alignment representation, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of California at Berkeley; Berkeley; USA |
NHGRI K22 HG00056; Searle Scholars program ; NIGMS P50 GM62412 |
PMID:15173120 | Free, Available for download, Freely available | nlx_156853, biotools:weblogo_3 | http://weblogo.threeplusone.com/ https://bio.tools/weblogo_3 |
SCR_010236 | WebLogo Version 2.8.2, WebLogo3, WebLogo | 2026-02-17 10:01:40 | 3653 | |||||
|
Pathema Resource Report Resource Website 1+ mentions |
Pathema (RRID:SCR_010585) | Pathema | data or information resource, production service resource, analysis service resource, database, service resource, data analysis service | Pathema is one of the eight Bioinformatics Resource Centers designed to serve as a core resource for the bio-defense and infectious disease research community. Pathema strives to support basic research and accelerate scientific progress for understanding, detecting, diagnosing and treating an established set of six target NIAID Category A-C pathogens: Category A priority pathogens; Bacillus anthracis and Clostridium botulinum, and Category B priority pathogens; Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens and Entamoeba histolytica. Each target pathogen is represented in one of four distinct clade-specific Pathema web resources and underlying databases developed to target the specific data and analysis needs of each scientific community. All publicly available complete genome projects of phylogenetically related organisms are also represented, providing a comprehensive collection of organisms for comparative analyses. Pathema facilitates the scientific exploration of genomic and related data through its integration with web-based analysis tools, customized to obtain, display, and compute results relevant to ongoing pathogen research. Pathema serves the bio-defense and infectious disease research community by disseminating data resulting from pathogen genome sequencing projects and providing access to the results of inter-genomic comparisons for these organisms. The Pathema BRC contract ends in December 2009. At that time JCVI will cease maintenance of the Pathema web resource and data. The PATRIC team, located at the Virginia Bioinformatics Institute, created and maintains a consolidated BRC for all of the NIAID category A-C priority pathogenic bacteria. The EuPathDB team at the University of Pennsylvania will support all eukaryotic pathogens. Pathema transferred all data and software to PATRIC and EuPathDB for incorporation into their new Web-based bioinformatics resource. | bacillus anthracis, clostridium botulinum, burkholderia mallei, burkholderia pseudomallei, clostridium perfringens, entamoeba histolytica, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: J. Craig Venter Institute |
NIAID contract HHSN266200400038C | PMID:19843611 | biotools:pathema, nlx_45829 | https://bio.tools/pathema | SCR_010585 | Pathema Genome Resource, Pathema Bioinformatics Resource Center | 2026-02-17 10:01:31 | 6 | |||||
|
icy Resource Report Resource Website 100+ mentions |
icy (RRID:SCR_010587) | ICY | software development environment, software development tool, software application, image processing software, data processing software, source code, software resource, service resource, software repository, image analysis software | An open community platform for bioimage informatics providing the software resources to visualize, annotate and quantify bioimaging data. To bridge the gap between developers and users, it combines: a) an open-source image analysis software, offering a powerful and flexible environment for developers such as applied mathematicians to write algorithms fast and efficiently; b) a common set of tools to view and manipulate data, and a set of plugins to perform specific quantification or analysis on images; c) a community-based website centralizing all plugins and resources to facilitate their management and maximize their visibility towards users. Workspaces are virtual groups of plugins dedicated to a specific application or image processing domain. By downloading a workspace, ICY automatically installs all corresponding plugins. The workspaces are enabled, but the editing section is not ready yet. If you want to publish a plugin on this website, its code has to be GPL. Source code is available and provided in each application download. | image analysis, microscopy, javascript, python, plugin, protocol, script, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Pasteur Institute |
Centre National de la Recherche Scientifique ; French National Research Agency ANR-10-INBS-04-06 |
PMID:22743774 | Free, Open unspecified license, GNU General Public License, v3, The community can contribute to this resource | biotools:icy, nlx_45928 | https://bio.tools/icy | SCR_010587 | icy bioimage analysis | 2026-02-17 10:01:48 | 320 | ||||
|
Geneious Resource Report Resource Website 10000+ mentions |
Geneious (RRID:SCR_010519) | data management software, software application, data processing software, data analysis software, sequence analysis software, software resource, software toolkit | Software package for sequence alignment, assembly and analysis. Integrated and extendable desktop software platform for organization and analysis of sequence data. Bioinformatics software platform packed with molecular biology and sequence analysis tools. | Sequence alignment software, data management software, analysis software, Geneious Biologics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is parent organization of: Geneious Microsatellite Plugin |
PMID:22543367 | Restricted | OMICS_00016, biotools:geneious | http://nebc.nerc.ac.uk/news/geneiousonbl https://bio.tools/geneious |
SCR_010519 | Geneious Prime, Geneious 11.0, Geneious 11.1.2, Geneious 8.1, Geneious Basic | 2026-02-17 10:01:54 | 12252 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant 2U24DK097771-09.
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